JEDLIČKA, Pavel, Matej LEXA, Ivan VANÁT, Eduard KEJNOVSKÝ and Roman HOBZA. Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study. Mobile DNA, 2019, vol. 10, No 1, p. 1-14. ISSN 1759-8753. doi:10.1186/s13100-019-0186-z.
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Basic information
Original name Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study
Authors JEDLIČKA, Pavel (203 Czechia, guarantor), Matej LEXA (703 Slovakia, belonging to the institution), Ivan VANÁT (703 Slovakia, belonging to the institution), Eduard KEJNOVSKÝ (203 Czechia) and Roman HOBZA (203 Czechia).
Edition Mobile DNA, 2019, 1759-8753.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10611 Plant sciences, botany
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 3.161
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1186/s13100-019-0186-z
UT WoS 000502731200001
Keywords in English Transposable elements; LTR retrotransposons; Nesting; Chromatin; Nucleosomes; Plants
Tags International impact, Reviewed
Changed by Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 6/5/2020 17:12.
Abstract
Background:Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements.Results:We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family (“autoinsertions”). Nested LTR retrotransposons were preferentially located in the 3’UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons.Conclusions:We reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with allow negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.
Links
GA18-00258S, research and development projectName: Úloha transposonů v dynamice rostlinných genomů (Acronym: TRANSPOSONY_DRG)
Investor: Czech Science Foundation, Standard Projects
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